Question: ggplots gives errors
0
gravatar for ucheuna
2.4 years ago by
ucheuna0
ucheuna0 wrote:
Hey Mike, while following the time course experiments vignette, I continue to get an error when I use the code below: 
fiss <- plotCounts(ddsTC, which.min(resTC$padj), 
                   intgroup = c("minute","strain"), returnData = TRUE)
ggplot(fiss,
  aes(x = as.numeric(minute), y = count, color = strain, group = strain)) + 
  geom_point() + geom_smooth(se = FALSE, method = "loess") + scale_y_log10()

The error says: Error: could not find function "geom_point"

I intend to plot gene expression changes over time between wild type and knockout mice. This is a follow-up from yesterday's post. Thanks for your help.

 

rnaseq ggplot2 • 768 views
ADD COMMENTlink modified 2.4 years ago by Matthias Z.20 • written 2.4 years ago by ucheuna0

Probably a space issue. as @Matthias Z mentioned. I tried and its working fine. Maybe suggestion of representing the strain and minute in different shape and color.

geom_point(aes(color = strain, shape = minute))

Hope it helps!!

ADD REPLYlink written 2.4 years ago by Bio_Ram0
Answer: ggplots gives errors
0
gravatar for Matthias Z.
2.4 years ago by
Matthias Z.20
University Medical Center of Münster, Germany
Matthias Z.20 wrote:

Can you please post your

sessionInfo()

output? Because an improperly attached ggplot2 would be the most obvious reason. In case you copy and pasted above code you might also want to check, whether there is an irrgeular newline between )) +  and geom_point(), which could cause the trouble, too.

ADD COMMENTlink written 2.4 years ago by Matthias Z.20
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